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Papers of Note: Dec 14, 2010


Massive parallel DNA pyrosequencing analysis of the tumor suppressor BRG1/SMARCA4 in lung primary tumors.
Rodriguez-Nieto S, Cañada A, Pros E, Pinto AI, et al.
Hum Mutat. 2010 Dec 7. [Epub ahead of print]

W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
Lan X, Bonneville R, Apostolos J, Wu W, Jin VX.
Bioinformatics. 2010 Dec 7. [Epub ahead of print]

A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences.
Schwartz TS, Tae H, Yang Y, Mockaitis K, et al.
BMC Genomics. 2010 Dec 7;11(1):694. [Epub ahead of print]

Nanopore detection of 8-oxo-7,8-dihydro-2'-deoxyguanosine in immobilized single-stranded DNA via adduct formation to the DNA damage site.
Schibel AE, An N, Jin Q, Fleming AM, et al.
J Am Chem Soc. 2010 Dec 7. [Epub ahead of print]

Fabrication of nanopores for biomacromolecule detection.
Yao ZN, Wang KG, Jin AZ, Li JJ, et al.
J Nanosci Nanotechnol. 2010 Nov;10(11):7300-2.

Nanoporous platinum solid-state reference electrode with layer-by-layer polyelectrolyte junction for pH sensing chip.
Noh J, Park S, Boo H, Kim HC, Chung TD.
Lab Chip. 2010 Dec 7. [Epub ahead of print]

RSEQtools: A modular framework to analyze RNA-seq data using compact, anonymized data summaries.
Habegger L, Sboner A, Gianoulis TA, Rozowsky J, et al.Bioinformatics. 2010 Dec 5. [Epub ahead of print]

Overcoming methodical limits of standard RHD genotyping by next-generation sequencing.
Stabentheiner S, Danzer M, Niklas N, Atzmüller S, et al.
Vox Sang. 2010 Dec 7. doi: 10.1111/j.1423-0410.2010.01444.x.

DNA tunneling detector embedded in a nanopore.
Ivanov AP, Instuli E, McGilvery C, Baldwin G, et al.
Nano Lett. 2010 Dec 6. [Epub ahead of print]

The Scan

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.

Tumor Microenvironment Immune Score Provides Immunotherapy Response, Prognostic Insights

Using multiple in situ analyses and RNA sequence data, researchers in eBioMedicine have developed a score associated with immunotherapy response or survival.

CRISPR-Based Method for Finding Cancer-Associated Exosomal MicroRNAs in Blood

A team from China presents in ACS Sensors a liposome-mediated membrane fusion strategy for detecting miRNAs carried in exosomes in the blood with a CRISPR-mediated reporter system.

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.